From 4917252bb209e34f11b38c247407666ff208da2e Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 30 Jul 2013 16:11:08 +0000
Subject: [PATCH] table.sql file for new patch test database
---
.../homo_sapiens/patch/table.sql | 913 ++++++++++++++++++
1 file changed, 913 insertions(+)
create mode 100644 modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
new file mode 100644
index 0000000000..3781edc504
--- /dev/null
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -0,0 +1,913 @@
+CREATE TABLE alt_allele_attrib (alt_allele_id INT UNSIGNED,
+ attrib ENUM('IS_REPRESENTATIVE',
+ 'IS_MOST_COMMON_ALLELE',
+ 'IN_CORRECTED_ASSEMBLY',
+ 'HAS_CODING_POTENTIAL',
+ 'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY',
+ 'IN_SYNTENIC_REGION',
+ 'HAS_SAME_UNDERLYING_DNA_SEQUENCE',
+ 'IN_BROKEN_ASSEMBLY_REGION',
+ 'IS_VALID_ALTERNATE',
+ 'SAME_AS_REPRESENTATIVE',
+ 'SAME_AS_ANOTHER_ALLELE',
+ 'MANUALLY_ASSIGNED',
+ 'AUTOMATICALLY_ASSIGNED'),
+ KEY aa_idx (alt_allele_id,attrib)
+);
+
+CREATE TABLE alt_allele (alt_allele_id INT UNSIGNED AUTO_INCREMENT,
+ alt_allele_group_id INT UNSIGNED NOT NULL,
+ gene_id INT UNSIGNED NOT NULL,
+ PRIMARY KEY (alt_allele_id),
+ KEY (gene_id,alt_allele_group_id)
+ );
+
+CREATE TABLE alt_allele_group (alt_allele_group_id INT UNSIGNED AUTO_INCREMENT,
+ PRIMARY KEY (alt_allele_group_id)
+ );
+
+CREATE TABLE `analysis` (
+ `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+ `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+ `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `parameters` text COLLATE latin1_bin,
+ `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+ `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`analysis_id`),
+ UNIQUE KEY `logic_name` (`logic_name`),
+ KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `analysis_description` (
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `displayable` tinyint(1) NOT NULL DEFAULT '1',
+ `web_data` text COLLATE latin1_bin,
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `assembly` (
+ `asm_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `cmp_seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `asm_start` int(10) NOT NULL DEFAULT '0',
+ `asm_end` int(10) NOT NULL DEFAULT '0',
+ `cmp_start` int(10) NOT NULL DEFAULT '0',
+ `cmp_end` int(10) NOT NULL DEFAULT '0',
+ `ori` tinyint(4) NOT NULL DEFAULT '0',
+ UNIQUE KEY `all_idx` (`asm_seq_region_id`,`cmp_seq_region_id`,`asm_start`,`asm_end`,`cmp_start`,`cmp_end`,`ori`),
+ KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+ KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `assembly_exception` (
+ `assembly_exception_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
+ `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `ori` int(11) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`assembly_exception_id`),
+ KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `associated_group` (
+ `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `description` varchar(128) DEFAULT NULL,
+ PRIMARY KEY (`associated_group_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `associated_xref` (
+ `associated_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ `condition_type` varchar(128) DEFAULT NULL,
+ `associated_group_id` int(10) unsigned DEFAULT NULL,
+ `rank` int(10) unsigned DEFAULT '0',
+ PRIMARY KEY (`associated_xref_id`),
+ UNIQUE KEY `object_associated_source_type_idx` (`object_xref_id`,`xref_id`,`source_xref_id`,`condition_type`,`associated_group_id`),
+ KEY `associated_source_idx` (`source_xref_id`),
+ KEY `associated_object_idx` (`object_xref_id`),
+ KEY `associated_idx` (`xref_id`),
+ KEY `associated_group_idx` (`associated_group_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `attrib_type` (
+ `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`attrib_type_id`),
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `coord_system` (
+ `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `species_id` int(10) unsigned NOT NULL DEFAULT '1',
+ `name` varchar(40) NOT NULL,
+ `version` varchar(255) DEFAULT NULL,
+ `rank` int(11) NOT NULL,
+ `attrib` set('default_version','sequence_level') DEFAULT NULL,
+ PRIMARY KEY (`coord_system_id`),
+ UNIQUE KEY `rank_idx` (`rank`,`species_id`),
+ UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
+ KEY `species_idx` (`species_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `data_file` (
+ `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `coord_system_id` int(10) unsigned NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `name` varchar(100) NOT NULL,
+ `version_lock` tinyint(1) NOT NULL DEFAULT '0',
+ `absolute` tinyint(1) NOT NULL DEFAULT '0',
+ `url` text,
+ `file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
+ PRIMARY KEY (`data_file_id`),
+ UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
+ KEY `df_name_idx` (`name`),
+ KEY `df_analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `density_feature` (
+ `density_feature_id` int(11) NOT NULL AUTO_INCREMENT,
+ `density_type_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `density_value` float NOT NULL DEFAULT '0',
+ PRIMARY KEY (`density_feature_id`),
+ KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
+ KEY `seq_region_id_idx` (`seq_region_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `density_type` (
+ `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ `block_size` int(11) NOT NULL DEFAULT '0',
+ `region_features` int(11) NOT NULL DEFAULT '0',
+ `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
+ PRIMARY KEY (`density_type_id`),
+ UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `dependent_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL,
+ `master_xref_id` int(10) unsigned NOT NULL,
+ `dependent_xref_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`object_xref_id`),
+ KEY `dependent` (`dependent_xref_id`),
+ KEY `master_idx` (`master_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `ditag` (
+ `ditag_id` int(10) NOT NULL AUTO_INCREMENT,
+ `name` varchar(30) DEFAULT NULL,
+ `type` varchar(30) DEFAULT NULL,
+ `tag_count` smallint(6) DEFAULT '1',
+ `sequence` text,
+ PRIMARY KEY (`ditag_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `ditag_feature` (
+ `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `ditag_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ditag_pair_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `cigar_line` text,
+ `ditag_side` char(1) DEFAULT '',
+ PRIMARY KEY (`ditag_feature_id`),
+ KEY `ditag_id` (`ditag_id`),
+ KEY `ditag_pair_id` (`ditag_pair_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `dna` (
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumtext COLLATE latin1_bin NOT NULL,
+ PRIMARY KEY (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+
+CREATE TABLE `dna_align_feature` (
+ `dna_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_start` int(11) NOT NULL DEFAULT '0',
+ `hit_end` int(11) NOT NULL DEFAULT '0',
+ `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ `hcoverage` double DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `pair_dna_align_feature_id` int(10) unsigned DEFAULT NULL,
+ PRIMARY KEY (`dna_align_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
+ KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
+ KEY `hit_idx` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`),
+ KEY `pair_idx` (`pair_dna_align_feature_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=29797338 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `dnac` (
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `sequence` mediumblob NOT NULL,
+ `n_line` text COLLATE latin1_bin,
+ PRIMARY KEY (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
+
+CREATE TABLE `exon` (
+ `exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `phase` tinyint(2) NOT NULL,
+ `end_phase` tinyint(2) NOT NULL,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`exon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=162034 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `exon_transcript` (
+ `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `rank` int(10) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`exon_id`,`transcript_id`,`rank`),
+ KEY `transcript` (`transcript_id`),
+ KEY `exon` (`exon_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `external_db` (
+ `external_db_id` int(11) NOT NULL DEFAULT '0',
+ `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
+ `priority` int(11) NOT NULL DEFAULT '0',
+ `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `description` text COLLATE latin1_bin,
+ PRIMARY KEY (`external_db_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `external_synonym` (
+ `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ PRIMARY KEY (`xref_id`,`synonym`),
+ KEY `name_index` (`synonym`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `gene` (
+ `gene_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `biotype` varchar(40) NOT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_xref_id` int(10) unsigned DEFAULT NULL,
+ `source` varchar(20) NOT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `canonical_transcript_id` int(10) unsigned NOT NULL,
+ `canonical_annotation` varchar(255) DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`gene_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `xref_id_index` (`display_xref_id`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=18276 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `gene_archive` (
+ `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `gene_version` smallint(6) NOT NULL DEFAULT '0',
+ `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `transcript_version` smallint(6) NOT NULL DEFAULT '0',
+ `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `translation_version` smallint(6) NOT NULL DEFAULT '0',
+ `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
+ `mapping_session_id` int(11) NOT NULL DEFAULT '0',
+ KEY `gene_idx` (`gene_stable_id`,`gene_version`),
+ KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
+ KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `gene_attrib` (
+ `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ KEY `type_val_idx` (`attrib_type_id`,`value`),
+ KEY `gene_idx` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `identity_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `xref_identity` int(5) DEFAULT NULL,
+ `ensembl_identity` int(5) DEFAULT NULL,
+ `xref_start` int(11) DEFAULT NULL,
+ `xref_end` int(11) DEFAULT NULL,
+ `ensembl_start` int(11) DEFAULT NULL,
+ `ensembl_end` int(11) DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ PRIMARY KEY (`object_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `interpro` (
+ `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
+ KEY `id` (`id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `intron_supporting_evidence` (
+ `intron_supporting_evidence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `hit_name` varchar(100) NOT NULL,
+ `score` decimal(10,3) DEFAULT NULL,
+ `score_type` enum('NONE','DEPTH') DEFAULT 'NONE',
+ `is_splice_canonical` tinyint(1) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`intron_supporting_evidence_id`),
+ UNIQUE KEY `analysis_id` (`analysis_id`,`seq_region_id`,`seq_region_start`,`seq_region_end`,`seq_region_strand`,`hit_name`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `karyotype` (
+ `karyotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) NOT NULL DEFAULT '0',
+ `band` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `stain` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ PRIMARY KEY (`karyotype_id`),
+ KEY `region_band_idx` (`seq_region_id`,`band`)
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `map` (
+ `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
+ PRIMARY KEY (`map_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `mapping_session` (
+ `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
+ `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `created` datetime NOT NULL,
+ PRIMARY KEY (`mapping_session_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `mapping_set` (
+ `mapping_set_id` int(10) unsigned NOT NULL,
+ `internal_schema_build` varchar(20) NOT NULL,
+ `external_schema_build` varchar(20) NOT NULL,
+ PRIMARY KEY (`mapping_set_id`),
+ UNIQUE KEY `mapping_idx` (`internal_schema_build`,`external_schema_build`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `marker` (
+ `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
+ `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
+ `priority` int(11) DEFAULT NULL,
+ `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`marker_id`),
+ KEY `marker_idx` (`marker_id`,`priority`)
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `marker_feature` (
+ `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_weight` int(10) unsigned DEFAULT NULL,
+ PRIMARY KEY (`marker_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `marker_map_location` (
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `map_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `lod_score` double DEFAULT NULL,
+ PRIMARY KEY (`marker_id`,`map_id`),
+ KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `marker_synonym` (
+ `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+ `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`marker_synonym_id`),
+ KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
+ KEY `marker_idx` (`marker_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `meta` (
+ `meta_id` int(11) NOT NULL AUTO_INCREMENT,
+ `species_id` int(10) unsigned DEFAULT '1',
+ `meta_key` varchar(40) NOT NULL,
+ `meta_value` varchar(255) NOT NULL,
+ PRIMARY KEY (`meta_id`),
+ UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
+ KEY `species_value_idx` (`species_id`,`meta_value`)
+) ENGINE=MyISAM AUTO_INCREMENT=82 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `meta_coord` (
+ `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `coord_system_id` int(11) NOT NULL DEFAULT '0',
+ `max_length` int(11) DEFAULT NULL,
+ UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `misc_attrib` (
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ KEY `type_val_idx` (`attrib_type_id`,`value`),
+ KEY `misc_feature_idx` (`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `misc_feature` (
+ `misc_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `misc_feature_misc_set` (
+ `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `misc_set_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_feature_id`,`misc_set_id`),
+ KEY `reverse_idx` (`misc_set_id`,`misc_feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `misc_set` (
+ `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `description` text COLLATE latin1_bin NOT NULL,
+ `max_length` int(10) unsigned NOT NULL DEFAULT '0',
+ PRIMARY KEY (`misc_set_id`),
+ UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `object_xref` (
+ `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
+ `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `xref_id` int(10) unsigned NOT NULL,
+ `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
+ KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
+ KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
+) ENGINE=MyISAM AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `ontology_xref` (
+ `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `linkage_type` varchar(3) DEFAULT NULL,
+ `source_xref_id` int(10) unsigned DEFAULT NULL,
+ UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+ KEY `object_xref_id` (`object_xref_id`),
+ KEY `source_xref_id` (`source_xref_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `operon` (
+ `operon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`operon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `name_idx` (`display_label`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `operon_transcript` (
+ `operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `operon_id` int(10) unsigned NOT NULL,
+ `display_label` varchar(255) DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`operon_transcript_id`),
+ KEY `operon_idx` (`operon_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `operon_transcript_gene` (
+ `operon_transcript_id` int(10) unsigned DEFAULT NULL,
+ `gene_id` int(10) unsigned DEFAULT NULL,
+ KEY `operon_transcript_gene_idx` (`operon_transcript_id`,`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `peptide_archive` (
+ `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
+ `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+ `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
+ PRIMARY KEY (`peptide_archive_id`),
+ KEY `checksum` (`md5_checksum`)
+) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `prediction_exon` (
+ `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `prediction_transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `exon_rank` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `start_phase` tinyint(4) NOT NULL DEFAULT '0',
+ `score` double DEFAULT NULL,
+ `p_value` double DEFAULT NULL,
+ PRIMARY KEY (`prediction_exon_id`),
+ KEY `prediction_transcript_id` (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
+) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `prediction_transcript` (
+ `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) DEFAULT NULL,
+ `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`prediction_transcript_id`),
+ KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `protein_align_feature` (
+ `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double DEFAULT NULL,
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `cigar_line` text COLLATE latin1_bin,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ `hcoverage` double DEFAULT NULL,
+ PRIMARY KEY (`protein_align_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
+ KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
+ KEY `hit_idx` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `protein_feature` (
+ `protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `translation_id` int(11) NOT NULL DEFAULT '0',
+ `seq_start` int(10) NOT NULL DEFAULT '0',
+ `seq_end` int(10) NOT NULL DEFAULT '0',
+ `hit_start` int(10) NOT NULL DEFAULT '0',
+ `hit_end` int(10) NOT NULL DEFAULT '0',
+ `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double NOT NULL DEFAULT '0',
+ `evalue` double DEFAULT NULL,
+ `perc_ident` float DEFAULT NULL,
+ `external_data` text COLLATE latin1_bin,
+ `hit_description` text COLLATE latin1_bin,
+ PRIMARY KEY (`protein_feature_id`),
+ KEY `translation_id` (`translation_id`),
+ KEY `hitname_index` (`hit_name`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=242847 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `qtl` (
+ `qtl_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `trait` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `lod_score` float DEFAULT NULL,
+ `flank_marker_id_1` int(11) DEFAULT NULL,
+ `flank_marker_id_2` int(11) DEFAULT NULL,
+ `peak_marker_id` int(11) DEFAULT NULL,
+ PRIMARY KEY (`qtl_id`),
+ KEY `trait_idx` (`trait`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `qtl_feature` (
+ `seq_region_id` int(11) NOT NULL DEFAULT '0',
+ `seq_region_start` int(11) NOT NULL DEFAULT '0',
+ `seq_region_end` int(11) NOT NULL DEFAULT '0',
+ `qtl_id` int(11) NOT NULL DEFAULT '0',
+ `analysis_id` int(11) NOT NULL DEFAULT '0',
+ KEY `qtl_id` (`qtl_id`),
+ KEY `loc_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `qtl_synonym` (
+ `qtl_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `qtl_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `source_database` enum('rat genome database','ratmap') COLLATE latin1_bin NOT NULL DEFAULT 'rat genome database',
+ `source_primary_id` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ PRIMARY KEY (`qtl_synonym_id`),
+ KEY `qtl_idx` (`qtl_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `repeat_consensus` (
+ `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `repeat_consensus` text COLLATE latin1_bin,
+ PRIMARY KEY (`repeat_consensus_id`),
+ KEY `name` (`repeat_name`),
+ KEY `class` (`repeat_class`),
+ KEY `consensus` (`repeat_consensus`(10)),
+ KEY `type` (`repeat_type`)
+) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `repeat_feature` (
+ `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
+ `repeat_start` int(10) NOT NULL DEFAULT '0',
+ `repeat_end` int(10) NOT NULL DEFAULT '0',
+ `repeat_consensus_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double DEFAULT NULL,
+ PRIMARY KEY (`repeat_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `repeat_idx` (`repeat_consensus_id`),
+ KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `seq_region` (
+ `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `coord_system_id` int(10) NOT NULL DEFAULT '0',
+ `length` int(10) NOT NULL DEFAULT '0',
+ PRIMARY KEY (`seq_region_id`),
+ UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `seq_region_attrib` (
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ KEY `type_val_idx` (`attrib_type_id`,`value`),
+ KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `seq_region_mapping` (
+ `external_seq_region_id` int(10) unsigned NOT NULL,
+ `internal_seq_region_id` int(10) unsigned NOT NULL,
+ `mapping_set_id` int(10) unsigned NOT NULL,
+ KEY `mapping_set_id` (`mapping_set_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `seq_region_synonym` (
+ `seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `synonym` varchar(40) NOT NULL,
+ `external_db_id` smallint(5) unsigned DEFAULT NULL,
+ PRIMARY KEY (`seq_region_synonym_id`),
+ UNIQUE KEY `syn_idx` (`synonym`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `simple_feature` (
+ `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
+ `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
+ `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+ `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `score` double DEFAULT NULL,
+ PRIMARY KEY (`simple_feature_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `hit_idx` (`display_label`)
+) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `stable_id_event` (
+ `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `old_version` smallint(6) DEFAULT NULL,
+ `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
+ `new_version` smallint(6) DEFAULT NULL,
+ `mapping_session_id` int(10) NOT NULL DEFAULT '0',
+ `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `score` float NOT NULL DEFAULT '0',
+ UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
+ KEY `new_idx` (`new_stable_id`),
+ KEY `old_idx` (`old_stable_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `supporting_feature` (
+ `exon_id` int(11) NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
+ UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
+ KEY `feature_idx` (`feature_type`,`feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `transcript` (
+ `transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `gene_id` int(10) unsigned DEFAULT NULL,
+ `analysis_id` smallint(5) unsigned NOT NULL,
+ `seq_region_id` int(10) unsigned NOT NULL,
+ `seq_region_start` int(10) unsigned NOT NULL,
+ `seq_region_end` int(10) unsigned NOT NULL,
+ `seq_region_strand` tinyint(2) NOT NULL,
+ `display_xref_id` int(10) unsigned DEFAULT NULL,
+ `biotype` varchar(40) NOT NULL,
+ `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+ `description` text,
+ `is_current` tinyint(1) NOT NULL DEFAULT '1',
+ `canonical_translation_id` int(10) unsigned DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`transcript_id`),
+ UNIQUE KEY `canonical_translation_idx` (`canonical_translation_id`),
+ KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
+ KEY `gene_index` (`gene_id`),
+ KEY `xref_id_index` (`display_xref_id`),
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=21741 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `transcript_attrib` (
+ `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ KEY `type_val_idx` (`attrib_type_id`,`value`),
+ KEY `transcript_idx` (`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `transcript_intron_supporting_evidence` (
+ `transcript_id` int(10) unsigned NOT NULL,
+ `intron_supporting_evidence_id` int(10) unsigned NOT NULL,
+ `previous_exon_id` int(10) unsigned NOT NULL,
+ `next_exon_id` int(10) unsigned NOT NULL,
+ PRIMARY KEY (`intron_supporting_evidence_id`,`transcript_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `transcript_supporting_feature` (
+ `transcript_id` int(11) NOT NULL DEFAULT '0',
+ `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
+ `feature_id` int(11) NOT NULL DEFAULT '0',
+ UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
+ KEY `feature_idx` (`feature_type`,`feature_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+
+CREATE TABLE `translation` (
+ `translation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `start_exon_id` int(10) unsigned NOT NULL,
+ `seq_end` int(10) NOT NULL,
+ `end_exon_id` int(10) unsigned NOT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+ `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
+ PRIMARY KEY (`translation_id`),
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM AUTO_INCREMENT=21741 DEFAULT CHARSET=latin1;
+
+CREATE TABLE `translation_attrib` (
+ `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ KEY `type_val_idx` (`attrib_type_id`,`value`),
+ KEY `translation_idx` (`translation_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `unconventional_transcript_association` (
+ `transcript_id` int(10) unsigned NOT NULL,
+ `gene_id` int(10) unsigned NOT NULL,
+ `interaction_type` enum('antisense','sense_intronic','sense_overlaping_exonic','chimeric_sense_exonic') DEFAULT NULL,
+ KEY `transcript_id` (`transcript_id`),
+ KEY `gene_id` (`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `unmapped_object` (
+ `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
+ `analysis_id` int(10) unsigned NOT NULL,
+ `external_db_id` int(11) DEFAULT NULL,
+ `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
+ `unmapped_reason_id` smallint(5) unsigned NOT NULL,
+ `query_score` double DEFAULT NULL,
+ `target_score` double DEFAULT NULL,
+ `ensembl_id` int(10) unsigned DEFAULT '0',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+ `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`unmapped_object_id`),
+ KEY `id_idx` (`identifier`),
+ KEY `anal_idx` (`analysis_id`),
+ KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `unmapped_reason` (
+ `unmapped_reason_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+ PRIMARY KEY (`unmapped_reason_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
+CREATE TABLE `xref` (
+ `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `external_db_id` int(11) NOT NULL,
+ `dbprimary_acc` varchar(40) COLLATE latin1_bin NOT NULL,
+ `display_label` varchar(128) COLLATE latin1_bin NOT NULL,
+ `version` varchar(10) COLLATE latin1_bin NOT NULL DEFAULT '0',
+ `description` text COLLATE latin1_bin,
+ `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+ `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+ PRIMARY KEY (`xref_id`),
+ UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
+ KEY `display_index` (`display_label`),
+ KEY `info_type_idx` (`info_type`)
+) ENGINE=MyISAM AUTO_INCREMENT=1000006 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+
--
GitLab